From: shaila_at_biof.ufrj.br
Date: Wed Jun 22 2005 - 07:01:14 CDT
Hello!
While I was running my systems on different computers with different NAMD-
binaries I encountered following problem:
I use periodic boundary conditions and give the box-input in an xsc-file. (The
box-input is measured with vmd minmax/center.) When running my system with the
Linux- and Mac-binaries, however, the z-value of the cell origin is set to
zero. This does not happen with the Windows binary. Of course that is very
annoying as it scrambles up my cell and in the heating stage after my
minimisation the system stops because of margin violations.
Examples are below.
I fear that this could be an error in the binaries. Or could it be our way of
installing the binaries?
Of course I could try to center my system to 0/0/0 first, but then what is the
point of using the cellOrigin command at all (or here, more exactly, to give
the cell origin within xsc)? (And if I have to center my sytem to 0/0/0, how is
that done with vmd?)
Furthermore I would like to know which commands make sense to use in a
configuration file for minimisation. I have realised that, for example, the xst-
file is not written during a minimisation even if I give the commands (XSTfile,
XSTfrequency). So which commands does NAMD ignore when I use “minimize xxxx” in
the configuration file?
Thank you in advance,
Shaila Roessle
Example:
My xsc-file:
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
0 32.9779989242 0 0 0 32.2350008011 0 0 0 95.1359960556 -1.82473697662
0.905876851082 36.4296318054
(Of course, this system is very long in z, but it also happens with (closely)
cubic systems with a z0-value close to 0.)
Log-file of Linux
Info: NAMD 2.5 for Linux-i686
…
Info: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.5 Linux-i686 1 circe.cips.mpg.de fxj
Info: PERIODIC CELL BASIS 1 32.978 0 0
Info: PERIODIC CELL BASIS 2 0 32.235 0
Info: PERIODIC CELL BASIS 3 0 0 95.136
Info: PERIODIC CELL CENTER -1.82474 0.905877 0
Log-file of Mac
Charm++: standalone mode (not using charmrun)
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.5 for MacOSX-PPC
…
Info: Based on Charm++/Converse 050612 for net-ppc-darwin
Info: Built Fri Sep 26 17:25:29 CDT 2003 by jim on cupertino.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.5 MacOSX-PPC 1 nanomac.mpe-garching.mpg.de msi
…
Info: PERIODIC CELL BASIS 1 32.978 0 0
Info: PERIODIC CELL BASIS 2 0 32.235 0
Info: PERIODIC CELL BASIS 3 0 0 95.136
Info: PERIODIC CELL CENTER -1.82474 0.905877 0
Log-file of Windows
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.5 for Win32-i686
…
Info: Based on Charm++/Converse 050612 for net-win32-smp
Info: Running on 1 processors.
…
Info: PERIODIC CELL BASIS 1 32.978 0 0
Info: PERIODIC CELL BASIS 2 0 32.235 0
Info: PERIODIC CELL BASIS 3 0 0 95.136
Info: PERIODIC CELL CENTER -1.82474 0.905877 36.4296
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:52 CST